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How to annotate structural variants in VCF with esv/nsv identifiers
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15 months ago

Hi!

I'm struggling with finding a way to annotate a manta structural variants VCF output with SV regions identifiers from DGV/dbVAR (esv/nsv). Direct annotation based on the exact reported chromosomal positions certainly would not work as most of the structural variants have imprecise start-end locations. I did not manage to find the desired functionality in VEP, snpeff, annovar and loads of other tools reported elsewhere. I would appreciate any information on this issue.

Thanks! Kirill

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I have not used though but hope helps

https://github.com/brentp/vcfanno

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Thank you. Actually, I've come across this tool while googling but did not manage to comprehend its ability to do so. Now I do. I'll try it and post the result.

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vcfanno works very well, I can recommend it.

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I have found in house script to do that if you still need help I can help you

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